The Cipher Peon battle music has to be one of the most epic songs in all of the Pokemon games. That song helps emphasize how cruel Cipher's goals are destroying the Pokemon's feelings and turning them into cold, emotionless, fighting machines. It's also one of the main things that give Pokemon XD a serious theme.

I also like how Miror B was in both of those games. Having Ludicolos transferred over to XD and seeing all these Ludicolos dancing to Miror B's theme song is really fun. Even if he does ruin the serious theme to those games, it wouldn't be Pokemon without comic relief and he's one the most amusing characters in the Pokemon series.

Those games are so much better than the Pokemon Stadium series and Pokemon Battle Revolution could ever be. They don't have a cheesy announcer ruining things with annoying comments. It also has an actual plot that requires you to save the Shadow Pokemon before it's too late (although it technically can never be "too late"). You also fight with Pokemon that you actually own and can level them up within the game. The Simulation Battle CDs also made the game quite good (especially since the simulation battles have music that sounds so awesome that you don't even think it's from a Pokemon game).